At the top of the options dialog box is an option for the output format (Publication and MEGA) with the type of information that is output (distances) mentioned beneath. Below this is the option for outputting the distance data as a lower left triangular matrix or an upper right triangular matrix. On the right are options for specifying the number of decimal places for the pairwise distances in the output, and the maximum number of distances per line in the matrix.
When exporting to Excel or CSV you can choose to export as either a normal matrix or in a column format (Species 1, Species 2, Distance, Std Err.). The standard Matrix has a limit of 255 columns (that means 255 taxa) due to a limit imposed by Excel caused by a maximum number of columns.
In addition there are three buttons, one to print or save the output, one to quit the Options dialog box without exporting the data (Cancel), and the third to bring up the help file (this file). The Print/Save button brings up the Distances Display Box, where the distances are displayed as specified, with various options to edit, print and save the output.